In freshwater environments such as river and stream bottoms, rocks and submerged vegetation are covered with a biological felt (also called a periphyton, microbial mat, biofilm, etc.) that is susceptible to calcification. Compilation of an extensive bibliography and our own observations have allowed the identification of 44 species of Coccogonophyceae, 122 Hormogonophyceae, 2 Chrysophyceae, 35 Chlorophyceae, 3 Xanthophyceae, 2 diatoms, and 3 Rhodophyceae that grow on calcareous tufa and coat vegetation. Diverse genera include species that are also calcified but impossible to determine because they lack reproductive organs. Crystals have been described from 74 species in the literature and we have observed 53 others. They can be classified into 10 groups: (1) platelets on cell walls (Volvocales, analogues of coccolithophorids) (2) crystals in mucilage (Synechococcus, diatoms, Hydrurus) and calcified stalks (Oocardium) (3) sheaths containing crystals in the form of simple or three-branched needles, dendritic crystals, and crystals with box-work fabric (Geitleria, Scytonema) (4) sheaths containing calcite spherulites (5) stalks intersecting a large crystal (Cymbella) (6) micrite tubes (Phormidium, Schizothrix) (7) isolated rhombohedra (Zygnema, Scytonema), rhombohedra in clusters or chains (Nostoc parmelioides) (8) sparite platelets (Vaucheria) or isodiametric crystals (Scytonema, Chaetophora) (9) large crystals crosscut by many parallel filaments (Rivularia, Batrachospermum), and (10) fan-like crystals (Phormidium). These crystals can be arranged in clusters or form regular laminations. They can transform into isodiametric sparite crystals to form fan-like or radial palisadic structures. Knowledge of primary crystals and their diagenetic transformations is necessary to correctly interpret freshwater stromatolites. The latter always result from intense calcification and are a diagenetic transformation of a biological felt made of many prokaryotic and eukaryotic algal species, small invertebrates, and organic and mineral debris.